Estimation of Canopy Traits and Yield in Maize–Soybean Intercropping Systems Using UAV Multispectral Imagery and Machine Learning

Strip intercropping of maize and soybean is a key practice for improving land productivity and ensuring food and oil security in the hilly regions of the Loess Plateau. However, complex interspecific interactions generate highly heterogeneous canopy structures, making it difficult for traditional linear models to capture yield variability within mixed pixels. Based on a single-season (2025) field experiment, this study developed a UAV multispectral imagery-based yield estimation framework integrating multiple machine-learning algorithms. Shapley additive explanations (SHAP) and partial dependence plots (PDP) were used to interpret the spectral–yield relationships under different spatial configurations. The predictive performance of linear regression and eight nonlinear algorithms was compared using 20 spectral features. Ensemble learning outperformed linear approaches in all intercropping scenarios. In the maize–soybean 3:2 pattern, the GBDT model delivered the highest accuracy (R2 = 0.849; NRMSE = 9.28%), whereas in the 4:2 pattern with stronger shading stress on soybean, the random forest model showed the greatest robustness (R2 = 0.724). Interpretation results indicated that yield in monoculture systems was mainly driven by physiological traits characterized by visible-band indices, while yield in intercropping systems was dominated by structural and stress-response traits represented by near-infrared and soil-adjusted vegetation indices. The generated centimeter-scale yield maps revealed clear strip-like spatial variability driven by interspecific competition. Overall, explainable machine learning combined with UAV multispectral data shows promise for within-season yield estimation in intercropping systems and can support spatially differentiated precision management under the sampled conditions.